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I recently swapped/installed a used FB25 long block in a 2013 Forester 2.5 Forester X M/T. It starts and idles reliably, but seems to idle a little low. On throttle it just bogs down, and eventually stall. It does not seem to want to rev at all yet does not throw any codes. I have verified visually that the throttle body is opening and closing.

The used long block that I found had 45000KM and came from 2012 Forester with an A/T and came complete with plugs, injectors, rails, intake manifold, throttle body, map sensor. I did change the flywheel

It is the first time that I swap a motor, but I am confident about having restored all vacuum/fuel/electrical connections. Oil changed and subaru super coolant replaced too.

When you swapped the flex plate over to the flywheel did you get the crankshaft position plate (tone wheel) indexed properly on the crankshaft? It has a small pin to align it and is real easy to assemble it incorrectly.

When you swapped the flex plate over to the flywheel did you get the crankshaft position plate (tone wheel) indexed properly on the crankshaft? It has a small pin to align it and is real easy to assemble it incorrectly.

This.

This is exactly what the problem was

It is possible for the toning wheel/pin to become unaligned when placing and aligning the flywheel bolt holes